pybgen

pybgen is a Python (2 and 3) BGEN file parser and writer (not quite yet) released under the MIT licence.

For more information on how to use pybgen, refer to the API documentation. Below is a snippet describing the most common usage of the module.

from pybgen import PyBGEN

with PyBGEN("simple/data/example.32bits.bgen") as bgen:
    # Iterating over all variants
    for info, dosage in bgen:
        pass

    # Getting the genotypes of as single variant
    for info, dosage in bgen.get_variant("RSID_192"):
        print(info)
        print(dosage)